Starting phenix.real_space_refine on Fri Jul 3 13:42:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zyx_60582/07_2026/8zyx_60582.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zyx_60582/07_2026/8zyx_60582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zyx_60582/07_2026/8zyx_60582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zyx_60582/07_2026/8zyx_60582.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zyx_60582/07_2026/8zyx_60582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zyx_60582/07_2026/8zyx_60582.map" } resolution = 2.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.122 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 96 5.16 5 C 8959 2.51 5 N 2456 2.21 5 O 2993 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14508 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2990 Classifications: {'peptide': 387} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "B" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2990 Classifications: {'peptide': 387} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "C" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2990 Classifications: {'peptide': 387} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "D" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2990 Classifications: {'peptide': 387} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "F" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 948 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "J" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.14, per 1000 atoms: 0.22 Number of scatterers: 14508 At special positions: 0 Unit cell: (90.736, 108.712, 130.968, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 96 16.00 O 2993 8.00 N 2456 7.00 C 8959 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 193 " distance=2.02 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.02 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.02 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.03 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 193 " distance=2.02 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.02 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.03 Simple disulfide: pdb=" SG CYS C 175 " - pdb=" SG CYS C 193 " distance=2.02 Simple disulfide: pdb=" SG CYS C 183 " - pdb=" SG CYS C 230 " distance=2.02 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 280 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 337 " distance=2.04 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 447 " distance=2.03 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.04 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.06 Simple disulfide: pdb=" SG CYS D 175 " - pdb=" SG CYS D 193 " distance=2.02 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 230 " distance=2.02 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 237 " distance=2.03 Simple disulfide: pdb=" SG CYS D 278 " - pdb=" SG CYS D 291 " distance=2.03 Simple disulfide: pdb=" SG CYS D 280 " - pdb=" SG CYS D 289 " distance=2.03 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 337 " distance=2.04 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 447 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN I 4 " - " MAN I 5 " " MAN N 4 " - " MAN N 5 " " MAN R 4 " - " MAN R 5 " " MAN V 4 " - " MAN V 5 " ALPHA1-3 " BMA I 3 " - " MAN I 4 " " MAN I 6 " - " MAN I 7 " " BMA N 3 " - " MAN N 4 " " MAN N 6 " - " MAN N 7 " " BMA R 3 " - " MAN R 4 " " MAN R 6 " - " MAN R 7 " " BMA V 3 " - " MAN V 4 " " MAN V 6 " - " MAN V 7 " ALPHA1-6 " BMA I 3 " - " MAN I 6 " " BMA N 3 " - " MAN N 6 " " BMA R 3 " - " MAN R 6 " " BMA V 3 " - " MAN V 6 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " NAG-ASN " NAG A 501 " - " ASN A 86 " " NAG A 502 " - " ASN A 234 " " NAG B 501 " - " ASN B 86 " " NAG B 502 " - " ASN B 234 " " NAG C 501 " - " ASN C 86 " " NAG C 502 " - " ASN C 234 " " NAG D 501 " - " ASN D 86 " " NAG D 502 " - " ASN D 234 " " NAG E 1 " - " ASN A 146 " " NAG G 1 " - " ASN A 367 " " NAG H 1 " - " ASN A 329 " " NAG I 1 " - " ASN A 200 " " NAG K 1 " - " ASN B 146 " " NAG L 1 " - " ASN B 367 " " NAG M 1 " - " ASN B 329 " " NAG N 1 " - " ASN B 200 " " NAG O 1 " - " ASN C 146 " " NAG P 1 " - " ASN C 367 " " NAG Q 1 " - " ASN C 329 " " NAG R 1 " - " ASN C 200 " " NAG S 1 " - " ASN D 146 " " NAG T 1 " - " ASN D 367 " " NAG U 1 " - " ASN D 329 " " NAG V 1 " - " ASN D 200 " Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 642.9 milliseconds 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3202 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 31 sheets defined 3.3% alpha, 42.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 104 through 111 removed outlier: 4.471A pdb=" N GLY A 111 " --> pdb=" O ARG A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.609A pdb=" N ASN A 146 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 110 removed outlier: 3.572A pdb=" N ALA B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.517A pdb=" N ASN B 146 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 110 removed outlier: 3.604A pdb=" N ALA C 110 " --> pdb=" O ILE C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 146 Processing helix chain 'D' and resid 104 through 110 removed outlier: 3.538A pdb=" N ALA D 110 " --> pdb=" O ILE D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 146 removed outlier: 3.704A pdb=" N ASN D 146 " --> pdb=" O VAL D 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.987A pdb=" N THR F 91 " --> pdb=" O VAL F 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 84 removed outlier: 3.972A pdb=" N PHE J 84 " --> pdb=" O PRO J 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 102 removed outlier: 5.373A pdb=" N PHE A 97 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N THR A 449 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N CYS A 447 " --> pdb=" O PRO A 99 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ARG A 420 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.704A pdb=" N TRP A 115 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THR A 138 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N THR A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLN A 136 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 157 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N CYS A 175 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N MET A 160 " --> pdb=" O GLN A 173 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLN A 173 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 184 removed outlier: 6.644A pdb=" N ALA A 201 " --> pdb=" O VAL A 216 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL A 216 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA A 203 " --> pdb=" O SER A 214 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER A 214 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N PHE A 205 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 233 removed outlier: 3.776A pdb=" N VAL A 231 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLU A 258 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ILE A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 276 through 283 removed outlier: 5.457A pdb=" N GLU A 277 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG A 292 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 356 removed outlier: 4.500A pdb=" N TRP A 352 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY A 363 " --> pdb=" O TRP A 352 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ASP A 402 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N GLU A 375 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 10.420A pdb=" N ARG A 400 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 11.318A pdb=" N PHE A 377 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 13.266A pdb=" N VAL A 398 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 15.896A pdb=" N VAL A 379 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 16.232A pdb=" N VAL A 396 " --> pdb=" O VAL A 379 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 96 through 102 removed outlier: 5.198A pdb=" N PHE B 97 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N THR B 449 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N CYS B 447 " --> pdb=" O PRO B 99 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ARG B 420 " --> pdb=" O GLY B 448 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.782A pdb=" N TRP B 115 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N THR B 138 " --> pdb=" O TRP B 115 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N THR B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLN B 136 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU B 158 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS B 172 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 179 through 184 removed outlier: 6.534A pdb=" N TYR B 207 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU B 211 " --> pdb=" O TYR B 207 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 231 through 233 removed outlier: 3.772A pdb=" N VAL B 231 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU B 258 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ILE B 262 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 276 through 283 removed outlier: 5.618A pdb=" N GLU B 277 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ARG B 292 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B 311 " --> pdb=" O ASN B 306 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 352 through 356 removed outlier: 4.545A pdb=" N TRP B 352 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY B 363 " --> pdb=" O TRP B 352 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU B 372 " --> pdb=" O ASP B 399 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ASP B 399 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N TYR B 374 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS B 378 " --> pdb=" O ASN B 393 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ASN B 393 " --> pdb=" O LYS B 378 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 102 removed outlier: 3.699A pdb=" N GLY C 96 " --> pdb=" O THR C 449 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL C 445 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS C 102 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ILE C 443 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ARG C 420 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 115 through 124 removed outlier: 4.711A pdb=" N TRP C 115 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N THR C 138 " --> pdb=" O TRP C 115 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N THR C 117 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLN C 136 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLU C 119 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU C 134 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR C 157 " --> pdb=" O GLY C 135 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU C 158 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS C 172 " --> pdb=" O MET C 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 179 through 184 removed outlier: 6.422A pdb=" N TYR C 207 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LEU C 211 " --> pdb=" O TYR C 207 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 231 through 233 removed outlier: 3.683A pdb=" N VAL C 231 " --> pdb=" O THR C 238 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU C 258 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ILE C 262 " --> pdb=" O GLU C 258 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 276 through 283 removed outlier: 5.386A pdb=" N GLU C 277 " --> pdb=" O ARG C 292 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG C 292 " --> pdb=" O GLU C 277 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 353 through 356 removed outlier: 6.794A pdb=" N LEU C 372 " --> pdb=" O ASP C 399 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ASP C 399 " --> pdb=" O LEU C 372 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N TYR C 374 " --> pdb=" O ILE C 397 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LYS C 378 " --> pdb=" O ASN C 393 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ASN C 393 " --> pdb=" O LYS C 378 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 96 through 102 removed outlier: 3.667A pdb=" N GLY D 96 " --> pdb=" O THR D 449 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL D 445 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LYS D 102 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE D 443 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ARG D 420 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 115 through 124 removed outlier: 4.735A pdb=" N TRP D 115 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N THR D 138 " --> pdb=" O TRP D 115 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N THR D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLN D 136 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR D 157 " --> pdb=" O GLY D 135 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU D 158 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS D 172 " --> pdb=" O MET D 160 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 179 through 184 removed outlier: 6.538A pdb=" N TYR D 207 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N LEU D 211 " --> pdb=" O TYR D 207 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 231 through 233 removed outlier: 3.711A pdb=" N VAL D 231 " --> pdb=" O THR D 238 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLU D 258 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE D 262 " --> pdb=" O GLU D 258 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 276 through 283 removed outlier: 5.358A pdb=" N GLU D 277 " --> pdb=" O ARG D 292 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ARG D 292 " --> pdb=" O GLU D 277 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 352 through 356 removed outlier: 4.491A pdb=" N TRP D 352 " --> pdb=" O GLY D 363 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY D 363 " --> pdb=" O TRP D 352 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU D 372 " --> pdb=" O ASP D 399 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ASP D 399 " --> pdb=" O LEU D 372 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N TYR D 374 " --> pdb=" O ILE D 397 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS D 378 " --> pdb=" O ASN D 393 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ASN D 393 " --> pdb=" O LYS D 378 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC8, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.600A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 11 through 12 Processing sheet with id=AD1, first strand: chain 'F' and resid 101 through 102 Processing sheet with id=AD2, first strand: chain 'J' and resid 11 through 13 removed outlier: 6.725A pdb=" N LEU J 34 " --> pdb=" O ASP J 50 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ASP J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 11 through 13 Processing sheet with id=AD4, first strand: chain 'J' and resid 19 through 24 447 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.52 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2553 1.32 - 1.45: 4390 1.45 - 1.58: 7756 1.58 - 1.71: 0 1.71 - 1.84: 116 Bond restraints: 14815 Sorted by residual: bond pdb=" CA SER A 388 " pdb=" CB SER A 388 " ideal model delta sigma weight residual 1.528 1.467 0.061 1.39e-02 5.18e+03 1.92e+01 bond pdb=" C SER C 228 " pdb=" O SER C 228 " ideal model delta sigma weight residual 1.235 1.191 0.044 1.02e-02 9.61e+03 1.83e+01 bond pdb=" CA SER B 388 " pdb=" CB SER B 388 " ideal model delta sigma weight residual 1.528 1.467 0.060 1.58e-02 4.01e+03 1.46e+01 bond pdb=" CA TYR D 130 " pdb=" C TYR D 130 " ideal model delta sigma weight residual 1.523 1.483 0.040 1.18e-02 7.18e+03 1.15e+01 bond pdb=" C CYS D 129 " pdb=" O CYS D 129 " ideal model delta sigma weight residual 1.235 1.195 0.039 1.18e-02 7.18e+03 1.11e+01 ... (remaining 14810 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 19743 2.96 - 5.92: 312 5.92 - 8.87: 40 8.87 - 11.83: 3 11.83 - 14.79: 3 Bond angle restraints: 20101 Sorted by residual: angle pdb=" N PRO B 386 " pdb=" CA PRO B 386 " pdb=" C PRO B 386 " ideal model delta sigma weight residual 111.41 96.62 14.79 1.50e+00 4.44e-01 9.72e+01 angle pdb=" N PRO A 386 " pdb=" CA PRO A 386 " pdb=" C PRO A 386 " ideal model delta sigma weight residual 111.22 98.44 12.78 1.40e+00 5.10e-01 8.33e+01 angle pdb=" N ARG D 430 " pdb=" CA ARG D 430 " pdb=" C ARG D 430 " ideal model delta sigma weight residual 110.50 120.60 -10.10 1.41e+00 5.03e-01 5.13e+01 angle pdb=" CA ASN C 146 " pdb=" CB ASN C 146 " pdb=" CG ASN C 146 " ideal model delta sigma weight residual 112.60 118.70 -6.10 1.00e+00 1.00e+00 3.72e+01 angle pdb=" C ARG C 283 " pdb=" CA ARG C 283 " pdb=" CB ARG C 283 " ideal model delta sigma weight residual 112.09 120.78 -8.69 1.43e+00 4.89e-01 3.69e+01 ... (remaining 20096 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.94: 8857 25.94 - 51.88: 514 51.88 - 77.82: 96 77.82 - 103.76: 59 103.76 - 129.70: 45 Dihedral angle restraints: 9571 sinusoidal: 4535 harmonic: 5036 Sorted by residual: dihedral pdb=" CB CYS B 183 " pdb=" SG CYS B 183 " pdb=" SG CYS B 230 " pdb=" CB CYS B 230 " ideal model delta sinusoidal sigma weight residual -86.00 -170.98 84.98 1 1.00e+01 1.00e-02 8.76e+01 dihedral pdb=" CB CYS C 183 " pdb=" SG CYS C 183 " pdb=" SG CYS C 230 " pdb=" CB CYS C 230 " ideal model delta sinusoidal sigma weight residual -86.00 -170.46 84.46 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CB CYS D 183 " pdb=" SG CYS D 183 " pdb=" SG CYS D 230 " pdb=" CB CYS D 230 " ideal model delta sinusoidal sigma weight residual -86.00 -165.93 79.93 1 1.00e+01 1.00e-02 7.92e+01 ... (remaining 9568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 2256 0.114 - 0.228: 87 0.228 - 0.342: 15 0.342 - 0.456: 2 0.456 - 0.570: 4 Chirality restraints: 2364 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-02 2.50e+03 7.82e+02 chirality pdb=" C1 MAN V 4 " pdb=" O3 BMA V 3 " pdb=" C2 MAN V 4 " pdb=" O5 MAN V 4 " both_signs ideal model delta sigma weight residual False 2.40 2.11 0.29 2.00e-02 2.50e+03 2.04e+02 chirality pdb=" C1 MAN V 7 " pdb=" O3 MAN V 6 " pdb=" C2 MAN V 7 " pdb=" O5 MAN V 7 " both_signs ideal model delta sigma weight residual False 2.40 2.14 0.26 2.00e-02 2.50e+03 1.71e+02 ... (remaining 2361 not shown) Planarity restraints: 2535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 502 " -0.150 2.00e-02 2.50e+03 1.23e-01 1.88e+02 pdb=" C7 NAG C 502 " 0.048 2.00e-02 2.50e+03 pdb=" C8 NAG C 502 " -0.113 2.00e-02 2.50e+03 pdb=" N2 NAG C 502 " 0.193 2.00e-02 2.50e+03 pdb=" O7 NAG C 502 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 2 " 0.139 2.00e-02 2.50e+03 1.15e-01 1.64e+02 pdb=" C7 NAG O 2 " -0.048 2.00e-02 2.50e+03 pdb=" C8 NAG O 2 " 0.107 2.00e-02 2.50e+03 pdb=" N2 NAG O 2 " -0.179 2.00e-02 2.50e+03 pdb=" O7 NAG O 2 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " -0.133 2.00e-02 2.50e+03 1.10e-01 1.50e+02 pdb=" C7 NAG M 2 " 0.041 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " -0.100 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " 0.174 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " 0.018 2.00e-02 2.50e+03 ... (remaining 2532 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 117 2.55 - 3.14: 11022 3.14 - 3.72: 24194 3.72 - 4.31: 37387 4.31 - 4.90: 59510 Nonbonded interactions: 132230 Sorted by model distance: nonbonded pdb=" O ASP A 293 " pdb="CA CA A 503 " model vdw 1.959 3.250 nonbonded pdb=" O ASP D 293 " pdb="CA CA D 503 " model vdw 1.982 3.250 nonbonded pdb=" O HIS A 347 " pdb="CA CA A 503 " model vdw 2.046 3.250 nonbonded pdb=" O ASP C 293 " pdb="CA CA C 503 " model vdw 2.062 3.250 nonbonded pdb=" O HIS B 347 " pdb="CA CA B 503 " model vdw 2.153 3.250 ... (remaining 132225 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'I' selection = chain 'N' selection = chain 'R' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.370 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 14913 Z= 0.335 Angle : 1.042 18.486 20357 Z= 0.553 Chirality : 0.061 0.570 2364 Planarity : 0.014 0.432 2511 Dihedral : 20.045 129.696 6255 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.17 % Favored : 96.77 % Rotamer: Outliers : 0.46 % Allowed : 16.47 % Favored : 83.07 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 13.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.20), residues: 1766 helix: -0.75 (0.92), residues: 24 sheet: 0.15 (0.20), residues: 684 loop : -0.51 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 210 TYR 0.014 0.002 TYR B 155 PHE 0.013 0.002 PHE A 354 TRP 0.015 0.002 TRP B 178 HIS 0.011 0.001 HIS C 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.32 (14815) covalent geometry : angle 0.90593 / 0.53 (20101) SS BOND : bond 0.00590 / 0.30 ( 38) SS BOND : angle 1.34971 / 0.92 ( 76) hydrogen bonds : bond 0.20898 / 14.15 ( 437) hydrogen bonds : angle 9.15962 / 6.33 ( 1209) link_ALPHA1-2 : bond 0.02608 / 1.30 ( 4) link_ALPHA1-2 : angle 4.89717 / 2.55 ( 12) link_ALPHA1-3 : bond 0.02219 / 1.08 ( 8) link_ALPHA1-3 : angle 5.10729 / 2.81 ( 24) link_ALPHA1-6 : bond 0.02105 / 1.05 ( 4) link_ALPHA1-6 : angle 1.69229 / 0.83 ( 12) link_BETA1-4 : bond 0.04103 / 2.13 ( 20) link_BETA1-4 : angle 6.10579 / 4.13 ( 60) link_NAG-ASN : bond 0.00921 / 0.48 ( 24) link_NAG-ASN : angle 5.61290 / 3.79 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 183 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ASN cc_start: 0.8142 (OUTLIER) cc_final: 0.7837 (p0) REVERT: A 381 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8027 (mt-10) REVERT: A 390 LEU cc_start: 0.8777 (tp) cc_final: 0.8443 (tp) REVERT: C 387 LYS cc_start: 0.8161 (mtpt) cc_final: 0.7615 (mptt) REVERT: C 391 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8324 (tt0) REVERT: C 415 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.7981 (tppt) REVERT: C 435 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8398 (pm20) REVERT: D 210 ARG cc_start: 0.8369 (mtt90) cc_final: 0.8124 (mtt90) REVERT: F 3 GLN cc_start: 0.8452 (tt0) cc_final: 0.8072 (tt0) REVERT: F 21 SER cc_start: 0.8752 (m) cc_final: 0.8232 (p) REVERT: F 33 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8187 (mm-30) REVERT: J 104 LEU cc_start: 0.7876 (mp) cc_final: 0.7630 (mp) outliers start: 7 outliers final: 2 residues processed: 186 average time/residue: 0.6057 time to fit residues: 123.5906 Evaluate side-chains 179 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 172 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain C residue 391 GLN Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain J residue 75 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.0770 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 GLN B 385 ASN B 391 GLN C 273 GLN D 273 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.133558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.104692 restraints weight = 14611.612| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.67 r_work: 0.3106 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.0765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 14913 Z= 0.179 Angle : 0.773 12.108 20357 Z= 0.374 Chirality : 0.049 0.294 2364 Planarity : 0.005 0.090 2511 Dihedral : 16.480 121.644 3170 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.82 % Allowed : 16.08 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.20), residues: 1766 helix: -0.02 (0.85), residues: 28 sheet: 0.50 (0.21), residues: 627 loop : -0.58 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 150 TYR 0.012 0.002 TYR B 121 PHE 0.013 0.002 PHE B 410 TRP 0.014 0.002 TRP B 178 HIS 0.007 0.001 HIS C 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 (14815) covalent geometry : angle 0.71030 / 0.36 (20101) SS BOND : bond 0.00327 / 0.21 ( 38) SS BOND : angle 1.44599 / 0.95 ( 76) hydrogen bonds : bond 0.05290 / 3.52 ( 437) hydrogen bonds : angle 7.44127 / 5.12 ( 1209) link_ALPHA1-2 : bond 0.00987 / 0.50 ( 4) link_ALPHA1-2 : angle 2.91403 / 1.56 ( 12) link_ALPHA1-3 : bond 0.01694 / 0.79 ( 8) link_ALPHA1-3 : angle 4.23439 / 2.35 ( 24) link_ALPHA1-6 : bond 0.00461 / 0.23 ( 4) link_ALPHA1-6 : angle 1.72972 / 0.80 ( 12) link_BETA1-4 : bond 0.00809 / 0.52 ( 20) link_BETA1-4 : angle 2.92294 / 1.91 ( 60) link_NAG-ASN : bond 0.00376 / 0.20 ( 24) link_NAG-ASN : angle 3.26703 / 2.23 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8037 (mt-10) REVERT: A 390 LEU cc_start: 0.8827 (tp) cc_final: 0.8442 (tp) REVERT: C 387 LYS cc_start: 0.7774 (mtpt) cc_final: 0.7144 (mmtm) REVERT: C 415 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8035 (tppt) REVERT: D 128 LYS cc_start: 0.8426 (mtmp) cc_final: 0.8152 (ptpt) REVERT: D 210 ARG cc_start: 0.8450 (mtt90) cc_final: 0.8233 (mtt90) REVERT: D 249 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7592 (mtpp) REVERT: D 313 VAL cc_start: 0.8921 (t) cc_final: 0.8701 (t) REVERT: F 3 GLN cc_start: 0.8471 (tt0) cc_final: 0.8099 (tt0) REVERT: F 21 SER cc_start: 0.8885 (m) cc_final: 0.8374 (p) REVERT: F 33 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8032 (mm-30) REVERT: F 46 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8420 (tt0) outliers start: 28 outliers final: 17 residues processed: 192 average time/residue: 0.5787 time to fit residues: 121.5914 Evaluate side-chains 191 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 97 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 58 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 126 optimal weight: 0.0870 chunk 85 optimal weight: 0.9990 chunk 142 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 GLN B 391 GLN C 465 ASN D 273 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.134899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.106484 restraints weight = 14705.885| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.63 r_work: 0.3131 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14913 Z= 0.154 Angle : 0.707 9.958 20357 Z= 0.344 Chirality : 0.048 0.302 2364 Planarity : 0.004 0.044 2511 Dihedral : 13.750 117.950 3157 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.15 % Allowed : 16.41 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.20), residues: 1766 helix: 0.01 (0.89), residues: 28 sheet: 0.46 (0.21), residues: 636 loop : -0.59 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 150 TYR 0.012 0.002 TYR B 121 PHE 0.013 0.002 PHE B 354 TRP 0.014 0.001 TRP B 178 HIS 0.005 0.001 HIS F 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (14815) covalent geometry : angle 0.65738 / 0.33 (20101) SS BOND : bond 0.00325 / 0.20 ( 38) SS BOND : angle 0.94078 / 0.67 ( 76) hydrogen bonds : bond 0.04474 / 2.99 ( 437) hydrogen bonds : angle 7.03141 / 4.85 ( 1209) link_ALPHA1-2 : bond 0.01160 / 0.59 ( 4) link_ALPHA1-2 : angle 2.78492 / 1.45 ( 12) link_ALPHA1-3 : bond 0.01545 / 0.74 ( 8) link_ALPHA1-3 : angle 3.79784 / 2.06 ( 24) link_ALPHA1-6 : bond 0.00655 / 0.33 ( 4) link_ALPHA1-6 : angle 1.60110 / 0.74 ( 12) link_BETA1-4 : bond 0.00782 / 0.51 ( 20) link_BETA1-4 : angle 2.58977 / 1.68 ( 60) link_NAG-ASN : bond 0.00369 / 0.20 ( 24) link_NAG-ASN : angle 2.73456 / 1.89 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 CYS cc_start: 0.7561 (m) cc_final: 0.7359 (m) REVERT: A 381 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8061 (mt-10) REVERT: A 390 LEU cc_start: 0.8793 (tp) cc_final: 0.8433 (tp) REVERT: C 387 LYS cc_start: 0.7732 (mtpt) cc_final: 0.7106 (mmtm) REVERT: C 415 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8046 (tppt) REVERT: C 435 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8438 (pm20) REVERT: D 128 LYS cc_start: 0.8344 (mtmp) cc_final: 0.8127 (ptpt) REVERT: D 210 ARG cc_start: 0.8466 (mtt90) cc_final: 0.8232 (mtt90) REVERT: D 249 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7684 (mtpp) REVERT: F 3 GLN cc_start: 0.8449 (tt0) cc_final: 0.8091 (tt0) REVERT: F 21 SER cc_start: 0.8910 (m) cc_final: 0.8417 (p) REVERT: F 33 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8025 (mm-30) REVERT: F 82 GLN cc_start: 0.8924 (tp40) cc_final: 0.8715 (tp-100) REVERT: J 103 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7359 (tptm) outliers start: 33 outliers final: 19 residues processed: 197 average time/residue: 0.6288 time to fit residues: 135.9648 Evaluate side-chains 195 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 103 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 158 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 391 GLN C 273 GLN C 465 ASN D 273 GLN F 35 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.131652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.102692 restraints weight = 14578.679| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.66 r_work: 0.3084 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 14913 Z= 0.280 Angle : 0.810 9.597 20357 Z= 0.403 Chirality : 0.052 0.294 2364 Planarity : 0.005 0.046 2511 Dihedral : 13.159 116.787 3157 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.12 % Allowed : 15.36 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.19), residues: 1766 helix: -0.84 (0.84), residues: 24 sheet: 0.21 (0.20), residues: 662 loop : -0.58 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 428 TYR 0.016 0.003 TYR C 155 PHE 0.015 0.002 PHE B 354 TRP 0.017 0.002 TRP B 178 HIS 0.009 0.002 HIS F 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.28 (14815) covalent geometry : angle 0.75911 / 0.39 (20101) SS BOND : bond 0.00452 / 0.28 ( 38) SS BOND : angle 1.38332 / 0.96 ( 76) hydrogen bonds : bond 0.05306 / 3.55 ( 437) hydrogen bonds : angle 7.31029 / 5.03 ( 1209) link_ALPHA1-2 : bond 0.01205 / 0.61 ( 4) link_ALPHA1-2 : angle 2.35702 / 1.26 ( 12) link_ALPHA1-3 : bond 0.01537 / 0.76 ( 8) link_ALPHA1-3 : angle 4.04020 / 2.20 ( 24) link_ALPHA1-6 : bond 0.00498 / 0.25 ( 4) link_ALPHA1-6 : angle 1.99466 / 0.91 ( 12) link_BETA1-4 : bond 0.00715 / 0.46 ( 20) link_BETA1-4 : angle 2.76458 / 1.83 ( 60) link_NAG-ASN : bond 0.00631 / 0.32 ( 24) link_NAG-ASN : angle 3.01865 / 2.07 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 179 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7259 (t0) cc_final: 0.7049 (t0) REVERT: A 318 CYS cc_start: 0.7683 (m) cc_final: 0.7462 (m) REVERT: A 381 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8129 (mt-10) REVERT: A 390 LEU cc_start: 0.8832 (tp) cc_final: 0.8451 (tp) REVERT: A 430 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.6948 (tpp-160) REVERT: C 387 LYS cc_start: 0.7861 (mtpt) cc_final: 0.7192 (mptt) REVERT: C 391 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8638 (tt0) REVERT: C 415 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8010 (tppt) REVERT: C 432 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7566 (mp0) REVERT: C 435 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8431 (pm20) REVERT: D 210 ARG cc_start: 0.8581 (mtt90) cc_final: 0.8340 (mtt90) REVERT: D 249 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7652 (mtpp) REVERT: F 3 GLN cc_start: 0.8480 (tt0) cc_final: 0.8106 (tt0) REVERT: F 21 SER cc_start: 0.8910 (m) cc_final: 0.8445 (p) REVERT: F 33 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8286 (mm-30) outliers start: 48 outliers final: 25 residues processed: 210 average time/residue: 0.5757 time to fit residues: 132.9016 Evaluate side-chains 207 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 391 GLN Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 134 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 170 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 152 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 391 GLN C 273 GLN C 465 ASN D 173 GLN D 273 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.132918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.104112 restraints weight = 14652.121| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.66 r_work: 0.3107 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 14913 Z= 0.212 Angle : 0.741 9.569 20357 Z= 0.367 Chirality : 0.049 0.284 2364 Planarity : 0.004 0.044 2511 Dihedral : 12.774 115.569 3157 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.19 % Allowed : 16.67 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.19), residues: 1766 helix: -0.83 (0.84), residues: 24 sheet: 0.19 (0.20), residues: 650 loop : -0.49 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 150 TYR 0.013 0.002 TYR B 121 PHE 0.015 0.002 PHE B 354 TRP 0.017 0.002 TRP B 178 HIS 0.006 0.001 HIS F 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.21 (14815) covalent geometry : angle 0.69231 / 0.36 (20101) SS BOND : bond 0.00410 / 0.25 ( 38) SS BOND : angle 1.20467 / 0.83 ( 76) hydrogen bonds : bond 0.04736 / 3.18 ( 437) hydrogen bonds : angle 7.12231 / 4.90 ( 1209) link_ALPHA1-2 : bond 0.01120 / 0.57 ( 4) link_ALPHA1-2 : angle 2.30875 / 1.23 ( 12) link_ALPHA1-3 : bond 0.01481 / 0.73 ( 8) link_ALPHA1-3 : angle 3.93758 / 2.14 ( 24) link_ALPHA1-6 : bond 0.00541 / 0.27 ( 4) link_ALPHA1-6 : angle 1.68996 / 0.76 ( 12) link_BETA1-4 : bond 0.00736 / 0.49 ( 20) link_BETA1-4 : angle 2.52407 / 1.66 ( 60) link_NAG-ASN : bond 0.00424 / 0.22 ( 24) link_NAG-ASN : angle 2.80922 / 1.91 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 169 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7444 (t0) cc_final: 0.7175 (t0) REVERT: A 318 CYS cc_start: 0.7700 (m) cc_final: 0.7479 (m) REVERT: A 381 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8105 (mt-10) REVERT: A 390 LEU cc_start: 0.8823 (tp) cc_final: 0.8451 (tp) REVERT: A 415 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8320 (tttp) REVERT: A 430 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.6881 (tpp-160) REVERT: C 387 LYS cc_start: 0.7824 (mtpt) cc_final: 0.7132 (mptt) REVERT: C 415 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8019 (tppt) REVERT: C 435 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8411 (pm20) REVERT: D 210 ARG cc_start: 0.8561 (mtt90) cc_final: 0.8330 (mtt90) REVERT: D 249 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7663 (mtpp) REVERT: F 3 GLN cc_start: 0.8470 (tt0) cc_final: 0.8130 (tt0) REVERT: F 21 SER cc_start: 0.8932 (m) cc_final: 0.8454 (p) REVERT: F 33 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8206 (mm-30) REVERT: J 103 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7491 (tptm) outliers start: 49 outliers final: 25 residues processed: 200 average time/residue: 0.6251 time to fit residues: 136.9427 Evaluate side-chains 203 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 103 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 169 optimal weight: 0.0030 chunk 57 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 6 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 391 GLN C 273 GLN C 465 ASN D 173 GLN D 273 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.133940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.105246 restraints weight = 14702.783| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.67 r_work: 0.3118 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14913 Z= 0.170 Angle : 0.704 9.570 20357 Z= 0.347 Chirality : 0.048 0.287 2364 Planarity : 0.004 0.044 2511 Dihedral : 12.351 113.728 3157 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.60 % Allowed : 17.90 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.19), residues: 1766 helix: -0.28 (0.83), residues: 28 sheet: 0.17 (0.20), residues: 666 loop : -0.49 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 150 TYR 0.013 0.002 TYR B 121 PHE 0.015 0.002 PHE B 354 TRP 0.016 0.002 TRP B 178 HIS 0.005 0.001 HIS C 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (14815) covalent geometry : angle 0.66004 / 0.34 (20101) SS BOND : bond 0.00315 / 0.20 ( 38) SS BOND : angle 0.99148 / 0.70 ( 76) hydrogen bonds : bond 0.04292 / 2.88 ( 437) hydrogen bonds : angle 6.95565 / 4.79 ( 1209) link_ALPHA1-2 : bond 0.01104 / 0.57 ( 4) link_ALPHA1-2 : angle 2.42055 / 1.28 ( 12) link_ALPHA1-3 : bond 0.01467 / 0.72 ( 8) link_ALPHA1-3 : angle 3.85920 / 2.08 ( 24) link_ALPHA1-6 : bond 0.00549 / 0.27 ( 4) link_ALPHA1-6 : angle 1.61069 / 0.73 ( 12) link_BETA1-4 : bond 0.00740 / 0.49 ( 20) link_BETA1-4 : angle 2.36942 / 1.55 ( 60) link_NAG-ASN : bond 0.00438 / 0.22 ( 24) link_NAG-ASN : angle 2.56778 / 1.80 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 176 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASN cc_start: 0.7728 (OUTLIER) cc_final: 0.7064 (m-40) REVERT: A 309 ASP cc_start: 0.7486 (t0) cc_final: 0.7250 (t0) REVERT: A 318 CYS cc_start: 0.7727 (m) cc_final: 0.7513 (m) REVERT: A 381 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8069 (mt-10) REVERT: A 390 LEU cc_start: 0.8815 (tp) cc_final: 0.8464 (tp) REVERT: C 387 LYS cc_start: 0.7742 (mtpt) cc_final: 0.7041 (mptt) REVERT: C 415 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.7949 (tppt) REVERT: C 435 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8407 (pm20) REVERT: D 128 LYS cc_start: 0.8366 (mtmm) cc_final: 0.8141 (ptpt) REVERT: D 210 ARG cc_start: 0.8552 (mtt90) cc_final: 0.8303 (mtt90) REVERT: D 249 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7454 (mtpp) REVERT: D 430 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7949 (mmt180) REVERT: D 435 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8019 (mt-10) REVERT: F 3 GLN cc_start: 0.8474 (tt0) cc_final: 0.8149 (tt0) REVERT: F 21 SER cc_start: 0.8938 (m) cc_final: 0.8449 (p) REVERT: F 33 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8034 (mm-30) REVERT: J 103 LYS cc_start: 0.7691 (ttpt) cc_final: 0.7457 (tptm) outliers start: 40 outliers final: 23 residues processed: 200 average time/residue: 0.6084 time to fit residues: 133.4393 Evaluate side-chains 202 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 430 ARG Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 131 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 68 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 391 GLN C 273 GLN C 465 ASN D 147 ASN D 273 GLN D 306 ASN F 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.135655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.107428 restraints weight = 14677.481| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.65 r_work: 0.3155 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14913 Z= 0.139 Angle : 0.667 9.555 20357 Z= 0.327 Chirality : 0.047 0.284 2364 Planarity : 0.003 0.045 2511 Dihedral : 11.762 110.706 3157 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.41 % Allowed : 18.03 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.19), residues: 1766 helix: 0.01 (0.91), residues: 28 sheet: 0.34 (0.20), residues: 646 loop : -0.50 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 150 TYR 0.014 0.002 TYR B 121 PHE 0.014 0.002 PHE B 354 TRP 0.015 0.001 TRP B 178 HIS 0.004 0.001 HIS F 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (14815) covalent geometry : angle 0.62535 / 0.32 (20101) SS BOND : bond 0.00295 / 0.19 ( 38) SS BOND : angle 1.02567 / 0.69 ( 76) hydrogen bonds : bond 0.03837 / 2.56 ( 437) hydrogen bonds : angle 6.71640 / 4.63 ( 1209) link_ALPHA1-2 : bond 0.01234 / 0.64 ( 4) link_ALPHA1-2 : angle 2.56698 / 1.35 ( 12) link_ALPHA1-3 : bond 0.01475 / 0.71 ( 8) link_ALPHA1-3 : angle 3.80539 / 2.04 ( 24) link_ALPHA1-6 : bond 0.00577 / 0.29 ( 4) link_ALPHA1-6 : angle 1.60113 / 0.74 ( 12) link_BETA1-4 : bond 0.00758 / 0.50 ( 20) link_BETA1-4 : angle 2.21061 / 1.45 ( 60) link_NAG-ASN : bond 0.00348 / 0.18 ( 24) link_NAG-ASN : angle 2.27534 / 1.59 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 177 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASN cc_start: 0.7717 (OUTLIER) cc_final: 0.7052 (m-40) REVERT: A 381 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8048 (mt-10) REVERT: A 390 LEU cc_start: 0.8834 (tp) cc_final: 0.8498 (tp) REVERT: C 387 LYS cc_start: 0.7652 (mtpt) cc_final: 0.7025 (mmtm) REVERT: C 415 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.7954 (tppt) REVERT: C 435 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8409 (pm20) REVERT: D 210 ARG cc_start: 0.8455 (mtt90) cc_final: 0.8219 (mtt90) REVERT: D 249 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7408 (mtpp) REVERT: D 430 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7874 (mmt180) REVERT: D 435 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8056 (mt-10) REVERT: F 3 GLN cc_start: 0.8470 (tt0) cc_final: 0.8168 (tt0) REVERT: F 21 SER cc_start: 0.8940 (m) cc_final: 0.8474 (p) REVERT: F 33 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7868 (mm-30) REVERT: F 46 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8323 (tt0) outliers start: 37 outliers final: 19 residues processed: 196 average time/residue: 0.5764 time to fit residues: 123.9650 Evaluate side-chains 200 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 430 ARG Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 116 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 162 optimal weight: 0.0970 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 0.0980 chunk 1 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 391 GLN C 273 GLN C 465 ASN D 273 GLN D 306 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.135749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.107153 restraints weight = 14599.454| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.67 r_work: 0.3150 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14913 Z= 0.146 Angle : 0.671 9.943 20357 Z= 0.329 Chirality : 0.047 0.284 2364 Planarity : 0.004 0.043 2511 Dihedral : 11.384 108.277 3157 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.82 % Allowed : 19.01 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.19), residues: 1766 helix: -0.09 (0.88), residues: 28 sheet: 0.32 (0.20), residues: 646 loop : -0.48 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 150 TYR 0.013 0.002 TYR B 121 PHE 0.015 0.002 PHE B 354 TRP 0.014 0.001 TRP B 178 HIS 0.004 0.001 HIS F 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (14815) covalent geometry : angle 0.62886 / 0.32 (20101) SS BOND : bond 0.00293 / 0.18 ( 38) SS BOND : angle 0.99481 / 0.68 ( 76) hydrogen bonds : bond 0.03904 / 2.61 ( 437) hydrogen bonds : angle 6.70506 / 4.62 ( 1209) link_ALPHA1-2 : bond 0.01330 / 0.68 ( 4) link_ALPHA1-2 : angle 2.55224 / 1.33 ( 12) link_ALPHA1-3 : bond 0.01485 / 0.72 ( 8) link_ALPHA1-3 : angle 3.84790 / 2.07 ( 24) link_ALPHA1-6 : bond 0.00537 / 0.27 ( 4) link_ALPHA1-6 : angle 1.69579 / 0.79 ( 12) link_BETA1-4 : bond 0.00745 / 0.49 ( 20) link_BETA1-4 : angle 2.20336 / 1.45 ( 60) link_NAG-ASN : bond 0.00298 / 0.15 ( 24) link_NAG-ASN : angle 2.30451 / 1.62 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8062 (mt-10) REVERT: A 390 LEU cc_start: 0.8806 (tp) cc_final: 0.8480 (tp) REVERT: C 387 LYS cc_start: 0.7614 (mtpt) cc_final: 0.6988 (mmtm) REVERT: C 415 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8033 (tppt) REVERT: C 435 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8413 (pm20) REVERT: D 210 ARG cc_start: 0.8467 (mtt90) cc_final: 0.8218 (mtt90) REVERT: D 249 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7411 (mtpp) REVERT: D 387 LYS cc_start: 0.8294 (mttm) cc_final: 0.7930 (mttp) REVERT: F 3 GLN cc_start: 0.8486 (tt0) cc_final: 0.8179 (tt0) REVERT: F 21 SER cc_start: 0.8941 (m) cc_final: 0.8469 (p) REVERT: F 33 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7872 (mm-30) REVERT: F 46 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8348 (tt0) outliers start: 28 outliers final: 19 residues processed: 191 average time/residue: 0.6207 time to fit residues: 130.1597 Evaluate side-chains 194 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 142 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 159 optimal weight: 5.9990 chunk 156 optimal weight: 9.9990 chunk 139 optimal weight: 0.0570 chunk 151 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 391 GLN C 273 GLN C 465 ASN D 173 GLN D 273 GLN F 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.133150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.104154 restraints weight = 14572.152| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.66 r_work: 0.3105 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 14913 Z= 0.238 Angle : 0.762 9.966 20357 Z= 0.376 Chirality : 0.050 0.276 2364 Planarity : 0.004 0.045 2511 Dihedral : 11.447 107.553 3157 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.34 % Allowed : 18.62 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.19), residues: 1766 helix: -0.85 (0.83), residues: 24 sheet: 0.18 (0.20), residues: 666 loop : -0.45 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 150 TYR 0.014 0.002 TYR C 155 PHE 0.016 0.002 PHE B 354 TRP 0.015 0.002 TRP B 178 HIS 0.007 0.001 HIS F 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.24 (14815) covalent geometry : angle 0.71426 / 0.37 (20101) SS BOND : bond 0.00398 / 0.24 ( 38) SS BOND : angle 1.21275 / 0.86 ( 76) hydrogen bonds : bond 0.04764 / 3.19 ( 437) hydrogen bonds : angle 7.04007 / 4.85 ( 1209) link_ALPHA1-2 : bond 0.01450 / 0.74 ( 4) link_ALPHA1-2 : angle 2.23101 / 1.14 ( 12) link_ALPHA1-3 : bond 0.01513 / 0.74 ( 8) link_ALPHA1-3 : angle 4.19073 / 2.26 ( 24) link_ALPHA1-6 : bond 0.00425 / 0.21 ( 4) link_ALPHA1-6 : angle 1.97949 / 0.92 ( 12) link_BETA1-4 : bond 0.00727 / 0.47 ( 20) link_BETA1-4 : angle 2.40592 / 1.60 ( 60) link_NAG-ASN : bond 0.00560 / 0.28 ( 24) link_NAG-ASN : angle 2.82324 / 1.96 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASN cc_start: 0.7873 (OUTLIER) cc_final: 0.7277 (m-40) REVERT: A 318 CYS cc_start: 0.7770 (m) cc_final: 0.7547 (m) REVERT: A 381 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8119 (mt-10) REVERT: A 390 LEU cc_start: 0.8819 (tp) cc_final: 0.8458 (tp) REVERT: C 387 LYS cc_start: 0.7790 (mtpt) cc_final: 0.7131 (mmtm) REVERT: C 415 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8013 (tppt) REVERT: C 435 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8421 (pm20) REVERT: D 210 ARG cc_start: 0.8572 (mtt90) cc_final: 0.8318 (mtt90) REVERT: D 249 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7475 (mtpp) REVERT: D 387 LYS cc_start: 0.8324 (mttm) cc_final: 0.7919 (mttp) REVERT: D 430 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.8046 (mmt180) REVERT: D 435 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8000 (mt-10) REVERT: F 3 GLN cc_start: 0.8516 (tt0) cc_final: 0.8184 (tt0) REVERT: F 21 SER cc_start: 0.8964 (m) cc_final: 0.8474 (p) REVERT: F 33 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8200 (mm-30) REVERT: F 46 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8370 (tt0) outliers start: 36 outliers final: 21 residues processed: 196 average time/residue: 0.6071 time to fit residues: 130.9606 Evaluate side-chains 199 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 430 ARG Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 109 optimal weight: 0.0980 chunk 168 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 391 GLN C 273 GLN C 465 ASN D 273 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.135824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.107455 restraints weight = 14557.194| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.65 r_work: 0.3158 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14913 Z= 0.135 Angle : 0.668 9.504 20357 Z= 0.328 Chirality : 0.047 0.281 2364 Planarity : 0.003 0.043 2511 Dihedral : 10.851 105.422 3157 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.63 % Allowed : 19.60 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.20), residues: 1766 helix: -0.05 (0.89), residues: 28 sheet: 0.36 (0.20), residues: 670 loop : -0.46 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 150 TYR 0.014 0.002 TYR B 121 PHE 0.014 0.002 PHE B 354 TRP 0.015 0.001 TRP B 178 HIS 0.004 0.001 HIS B 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (14815) covalent geometry : angle 0.62601 / 0.32 (20101) SS BOND : bond 0.00257 / 0.16 ( 38) SS BOND : angle 0.87645 / 0.64 ( 76) hydrogen bonds : bond 0.03831 / 2.57 ( 437) hydrogen bonds : angle 6.73364 / 4.65 ( 1209) link_ALPHA1-2 : bond 0.01510 / 0.78 ( 4) link_ALPHA1-2 : angle 2.30716 / 1.14 ( 12) link_ALPHA1-3 : bond 0.01464 / 0.70 ( 8) link_ALPHA1-3 : angle 4.05527 / 2.18 ( 24) link_ALPHA1-6 : bond 0.00547 / 0.27 ( 4) link_ALPHA1-6 : angle 1.76750 / 0.81 ( 12) link_BETA1-4 : bond 0.00750 / 0.49 ( 20) link_BETA1-4 : angle 2.11819 / 1.40 ( 60) link_NAG-ASN : bond 0.00380 / 0.19 ( 24) link_NAG-ASN : angle 2.33873 / 1.64 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASN cc_start: 0.7711 (OUTLIER) cc_final: 0.7037 (m-40) REVERT: A 381 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8067 (mt-10) REVERT: A 390 LEU cc_start: 0.8809 (tp) cc_final: 0.8488 (tp) REVERT: C 387 LYS cc_start: 0.7575 (mtpt) cc_final: 0.6953 (mmtm) REVERT: C 415 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.7961 (tppt) REVERT: C 435 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8422 (pm20) REVERT: D 210 ARG cc_start: 0.8440 (mtt90) cc_final: 0.8196 (mtt90) REVERT: D 249 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7409 (mtpp) REVERT: D 387 LYS cc_start: 0.8319 (mttm) cc_final: 0.7969 (mttp) REVERT: D 430 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7918 (mmt180) REVERT: D 435 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8027 (mt-10) REVERT: F 3 GLN cc_start: 0.8482 (tt0) cc_final: 0.8185 (tt0) REVERT: F 21 SER cc_start: 0.8939 (m) cc_final: 0.8475 (p) REVERT: F 33 GLU cc_start: 0.8385 (mm-30) cc_final: 0.7908 (mm-30) REVERT: F 46 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8334 (tt0) outliers start: 25 outliers final: 16 residues processed: 183 average time/residue: 0.5830 time to fit residues: 117.1865 Evaluate side-chains 192 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 430 ARG Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 135 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 162 optimal weight: 0.0020 chunk 7 optimal weight: 0.7980 chunk 171 optimal weight: 9.9990 chunk 21 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 139 optimal weight: 7.9990 chunk 142 optimal weight: 10.0000 chunk 152 optimal weight: 1.9990 overall best weight: 0.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN B 391 GLN C 273 GLN C 465 ASN D 273 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.136898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.108205 restraints weight = 14523.637| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.68 r_work: 0.3162 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14913 Z= 0.138 Angle : 0.661 9.524 20357 Z= 0.324 Chirality : 0.047 0.276 2364 Planarity : 0.003 0.043 2511 Dihedral : 10.183 101.546 3154 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.69 % Allowed : 19.73 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.20), residues: 1766 helix: -0.05 (0.89), residues: 28 sheet: 0.29 (0.20), residues: 679 loop : -0.45 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 150 TYR 0.013 0.002 TYR B 121 PHE 0.015 0.002 PHE B 354 TRP 0.015 0.001 TRP B 178 HIS 0.004 0.001 HIS F 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (14815) covalent geometry : angle 0.61757 / 0.32 (20101) SS BOND : bond 0.00265 / 0.17 ( 38) SS BOND : angle 0.88914 / 0.64 ( 76) hydrogen bonds : bond 0.03769 / 2.51 ( 437) hydrogen bonds : angle 6.62198 / 4.56 ( 1209) link_ALPHA1-2 : bond 0.01505 / 0.78 ( 4) link_ALPHA1-2 : angle 2.36438 / 1.14 ( 12) link_ALPHA1-3 : bond 0.01426 / 0.68 ( 8) link_ALPHA1-3 : angle 4.13586 / 2.22 ( 24) link_ALPHA1-6 : bond 0.00595 / 0.30 ( 4) link_ALPHA1-6 : angle 1.89556 / 0.89 ( 12) link_BETA1-4 : bond 0.00742 / 0.48 ( 20) link_BETA1-4 : angle 2.08402 / 1.38 ( 60) link_NAG-ASN : bond 0.00385 / 0.19 ( 24) link_NAG-ASN : angle 2.29810 / 1.61 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5371.00 seconds wall clock time: 92 minutes 37.53 seconds (5557.53 seconds total)